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CompMetEng
GECKO
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GECKO 4.0.0b2
- #27
#27
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edkerk
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CompMetEng/GECKO:release/4.0.0b2
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Nov 2, 2026
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GECKO 4.0.0b2
#27
edkerk
merged 26 commits into
main
CompMetEng/GECKO:main
from
release/4.0.0b2
CompMetEng/GECKO:release/4.0.0b2
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Commits on Oct 4, 2026
fix: divide a BRENDA kcat by the substrate it was measured on (SysBioChalmers/GECKO#484)
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Let the BRENDA aggregation be chosen (SysBioChalmers/GECKO#485)
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Commits on Oct 15, 2026
Read the model adapter from model_adapter.toml, the file geckopy reads
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Read CatRange predictions returned as class ranges
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Commits on Oct 17, 2026
Merge pull request #1 from CompMetEng/feat/toml-adapter
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Merge pull request #2 from CompMetEng/fix/okp-catrange-ranges
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Point repository, documentation, version-check and CI links to CompMetEng (#8)
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Keep gathered kcats as kcat source files, one per source (#3)
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Assign kcats from the kcat source files, as model_adapter.toml sets (#9)
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Estimate kcats from the EC tree; make brenda_ec_tree the default preset (#10)
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Commits on Oct 19, 2026
Kcat strategies, BRENDA from toolbox-assets and GECKO 3 project upgrades (#11)
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Commits on Oct 23, 2026
feat: record the ecModel format and GECKO release in saved ecModels (#12)
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Commits on Oct 28, 2026
fix: give the same result as geckopy where the parity scenarios found differences (#13)
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getECstring: split EC numbers on semicolons as well as spaces (#14)
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Commits on Oct 30, 2026
sigmaFitter, getStandardKcat and getSubsetEcModel: plateau, subsystem case, empty subsystems, light ecModels (#15)
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Remove the references to the retired Bayesian kcat tuning (#16)
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Regenerate the HTML documentation (#17)
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Commits on Oct 31, 2026
loadProtData refuses a replicate count that does not match the file; calculateFfactor averages over the measured samples (#18)
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Add levelComplexConcs, getComplexFamilies and the perComplex option of flexibilizeEnzConcs (parity#131) (#19)
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getEnzymeBottlenecks ranks by the re-solved change of the objective (#20)
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Commits on Nov 1, 2026
Edge cases of GECKO agree with geckopy (#21)
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README: new GECKO logo, GECKO 4 and geckopy (#22)
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Require RAVEN 3.0.0 and ignore the pre-release suffix of the installed RAVEN (#24)
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Commits on Nov 2, 2026
getPfbaEnzymes: fractionOfOptimum for a negative optimum (#25)
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Keep version.txt and the README version off develop (#26)
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chore: version 4.0.0b2
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